How to set individual shadow catcher objects per render layer
This is my workaround about it:

I Used 3 frames and set the Shadow Catcher for every object in its frame.

Let the mouse pointer over the Shadow Catcher checkbox and press  I , this will make a keyframe to that single frame.

Move to the next frame, check the Shadow Catcher and with mouse pointer over the Shadow Catcher checkbox and press  I  again.

To the next frame, unckeck the Shadow Catcher and with mouse pointer over the Shadow Catcher checkbox and press  I  again.

Repest it to the other object. But using: frame 1 - unckeked, frame 2 - unchecked and frame 3 - checked.

Render the 3 frames an Animation.

See the image below: